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Singh RN, Sani RK. Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20. Microorganisms 2024; 12:960. [PMID: 38792789 PMCID: PMC11124144 DOI: 10.3390/microorganisms12050960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Noncoding RNAs (ncRNAs) play key roles in the regulation of important pathways, including cellular growth, stress management, signaling, and biofilm formation. Sulfate-reducing bacteria (SRB) contribute to huge economic losses causing microbial-induced corrosion through biofilms on metal surfaces. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation. This study aimed to identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20). Three in silico approaches revealed genome-wide distribution of 37 ncRNAs excluding tRNAs in the OA G20. These ncRNAs belonged to 18 different Rfam families. This study identified riboswitches, sRNAs, RNP, and SRP. The analysis revealed that these ncRNAs could play key roles in the regulation of several pathways of biosynthesis and transport involved in biofilm formation by OA G20. Three sRNAs, Pseudomonas P10, Hammerhead type II, and sX4, which were found in OA G20, are rare and their roles have not been determined in SRB. These results suggest that applying various computational methods could enrich the results and lead to the discovery of additional novel ncRNAs, which could lead to understanding the "rules of life of OA G20" during biofilm formation.
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Affiliation(s)
- Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD 57701, USA
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Interspecies Horizontal Transfer and Specific Integration of the Mosquitocidal Toxin-Encoding Plasmid pTAND672-2 from Bacillus thuringiensis subsp. israelensis to Lysinibacillus sphaericus. Appl Environ Microbiol 2023; 89:e0165222. [PMID: 36749061 PMCID: PMC9973010 DOI: 10.1128/aem.01652-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
pTAND672-2, a 144-kb resident plasmid of Bacillus thuringiensis serovar israelensis strain TAND672, was sequenced and characterized. This extrachromosomal element carries mosquitocidal toxin-, conjugation-, and recombinase-encoding genes, together with a putative arbitrium system, a genetic module recently discovered in temperate phages controlling lysogeny-lysis transition and in mobile genetic elements (MGEs) where its function remains clarified. Using conjugation experiments, pTAND672-2 is shown to be a novel integrative and conjugative element (ICE), which can horizontally transfer from B. thuringiensis serovar israelensis to Lysinibacillus sphaericus, another mosquitocidal bacterium, where it integrates into the chromosome. Its integration and circularization are reversible and involve a single-cross recombination between 33-bp specific sites, attB in the chromosome of L. sphaericus and attP in pTAND672-2. CDS143, coding for the putative tyrosine integrase Int143 distantly related to site-specific tyrosine Xer recombinases and phage integrases, can mediate the integration of pTAND672-2 to attB. The B. thuringiensis mosquito-killing genes carried by pTAND672-2 are efficiently transcribed and expressed in L. sphaericus, displaying a slight increased toxicity in this bacterium against Aedes albopictus larvae. The occurrence of pTAND672-2-like plasmids within the Bacillus cereus group was also explored and indicated that they all share a similar genetic backbone with diverse plasmid sizes, ranging from 58 to 225 kb. Interestingly, among them, the pEFR-4-4 plasmid of Bacillus paranthracis EFR-4 and p5 of B. thuringiensis BT-59 also display conjugative capability; moreover, like pTAND672-2 displays a chimeric structure between the pCH_133-e- and pBtoxis-like plasmids, pBTHD789-3 also appears to be mosaic of two plasmids. IMPORTANCE Horizontal transfer of mobile genetic elements carrying mosquitocidal toxin genes may play a driving role in the diversity of mosquitocidal bacteria. Here, the 144-kb mosquitocidal toxin-encoding plasmid pTAND672-2 is the first verified integrative and conjugative element (ICE) identified in Bacillus thuringiensis serovar israelensis. The key tyrosine integrase Int143, involved in the specific integration, is distantly related to other tyrosine recombinases. The study also reports the occurrence and potential interspecies transmission of pTAND672-2-like plasmids with varied sizes in B. thuringiensis, Bacillus paranthracis, and Bacillus wiedmannii isolates belonging to the Bacillus cereus group. This study is important for further understanding the evolution and ecology of mosquitocidal bacteria, as well as for providing new direction for the genetic engineering of biopesticides in the control of disease-transmitting mosquitoes.
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Fernanda Vázquez-Ramírez M, Ibarra JE, Edith Casados-Vázquez L, Eleazar Barboza-Corona J, Rincón-Castro MCD. Molecular and Toxicological Characterization of a Bacillus thuringiensis Strain Expressing a Vip3 Protein Highly Toxic to Spodoptera frugiperda (Lepidoptera: Noctuidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:1455-1463. [PMID: 35930375 DOI: 10.1093/jee/toac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The characterization of the Bacillus thuringiensis (Berliner) LBIT-418 strain was based on a previous work which indicated its high insecticidal potential. Therefore, toxicological, molecular, and biochemical characterizations were conducted in this work to identify its unique features and its potential to be developed as a bioinsecticide. This strain, originally isolated from a healthy mosquito larva, was identified within the subspecies kenyae by sequencing of the hag gene and by the multilocus sequence typing (MLST) technique. Genes cry1Ac2, cry1Ea3, cry2Aa1 and cry2Ab4, and a cry1Ia were detected in its genome, in addition to a vip3Aa gene. In this research, the latter protein was successfully cloned, expressed, and purified and showed high toxicity towards the fall armyworm, Spodoptera frugiperda (J.E. Smith), fourth instar larvae in bioassays using the microdroplet ingestion technique, estimating an LD50 of 21.38 ng/larva. Additional bioassays were performed using the diet surface inoculation technique of the strain's spore-crystal complex against diamondback moth larvae, Plutella xylostella (Linnaeus), estimating an LC50 of 10.22 ng/cm2. Its inability to produce β-exotoxin was demonstrated by bioassays against the nematode Caenorhabditis elegans Maupas and by HPLC analysis. These results support the high potential of this strain to be developed as a bioinsecticide.
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Affiliation(s)
- María Fernanda Vázquez-Ramírez
- Departamento de Alimentos, Posgrado en Biociencias, División de Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Ex Hacienda El Copal Km., Carretera Irapuato-León, Irapuato, Guanajuato, México
| | - Jorge E Ibarra
- Departamento de Biotecnología y Bioquímica, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, México
| | - Luz Edith Casados-Vázquez
- Departamento de Alimentos, Posgrado en Biociencias, División de Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Ex Hacienda El Copal Km., Carretera Irapuato-León, Irapuato, Guanajuato, México
| | - J Eleazar Barboza-Corona
- Departamento de Alimentos, Posgrado en Biociencias, División de Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Ex Hacienda El Copal Km., Carretera Irapuato-León, Irapuato, Guanajuato, México
| | - Ma Cristina Del Rincón-Castro
- Departamento de Alimentos, Posgrado en Biociencias, División de Ciencias de la Vida, Campus Irapuato-Salamanca, Universidad de Guanajuato, Ex Hacienda El Copal Km., Carretera Irapuato-León, Irapuato, Guanajuato, México
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Gupta M, Kumar H, Kaur S. Vegetative Insecticidal Protein (Vip): A Potential Contender From Bacillus thuringiensis for Efficient Management of Various Detrimental Agricultural Pests. Front Microbiol 2021; 12:659736. [PMID: 34054756 PMCID: PMC8158940 DOI: 10.3389/fmicb.2021.659736] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Bacillus thuringiensis (Bt) bacterium is found in various ecological habitats, and has natural entomo-pesticidal properties, due to the production of crystalline and soluble proteins during different growth phases. In addition to Cry and Cyt proteins, this bacterium also produces Vegetative insecticidal protein (Vip) during its vegetative growth phase, which is considered an excellent toxic candidate because of the difference in sequence homology and receptor sites from Cry proteins. Vip proteins are referred as second-generation insecticidal proteins, which can be used either alone or in complementarity with Cry proteins for the management of various detrimental pests. Among these Vip proteins, Vip1 and Vip2 act as binary toxins and have toxicity toward pests belonging to Hemiptera and Coleoptera orders, whereas the most important Vip3 proteins have insecticidal activity against Lepidopteran pests. These Vip3 proteins are similar to Cry proteins in terms of toxicity potential against susceptible insects. They are reported to be toxic toward pests, which can’t be controlled with Cry proteins. The Vip3 proteins have been successfully pyramided along with Cry proteins in transgenic rice, corn, and cotton to combat resistant pest populations. This review provides detailed information about the history and importance of Vip proteins, their types, structure, newly identified specific receptors, and action mechanism of this specific class of proteins. Various studies conducted on Vip proteins all over the world and the current status have been discussed. This review will give insights into the significance of Vip proteins as alternative promising candidate toxic proteins from Bt for the management of pests in most sustainable manner.
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Affiliation(s)
- Mamta Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.,ICAR-Indian Institute of Maize Research, Ludhiana, India
| | - Harish Kumar
- Punjab Agricultural University, Regional Research Station, Faridkot, India
| | - Sarvjeet Kaur
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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Genomics and Proteomics Analyses Revealed Novel Candidate Pesticidal Proteins in a Lepidopteran-Toxic Bacillus thuringiensis Strain. Toxins (Basel) 2020; 12:toxins12110673. [PMID: 33114565 PMCID: PMC7693509 DOI: 10.3390/toxins12110673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 11/17/2022] Open
Abstract
Discovery and identification of novel insecticidal proteins in Bacillus thuringiensis (Bt) strains are of crucial importance for efficient biological control of pests and better management of insect resistance. In this study, the Bt strain KhF, toxic for Plodia interpunctella and Grapholita molesta larvae, underwent genomics and proteomics analyses to achieve a better understanding of the bases of its pathogenicity. The whole-genome sequencing results revealed that the KhF strain contained nine coding sequences with homologies to Bt insecticidal genes. The lepidopteran toxic mixture of spores and crystals of this Bt strain was subjected to liquid chromatography and tandem mass spectrometry (LC-MS/MS) to assess the protein composition. The results of the proteomic analyses, combined with the toxin gene sequences, revealed that two of the main components of the crystals were two new candidate pesticidal proteins, named KhFA and KhFB. These proteins showed a similarity lower than 36% to the other known Bt toxins. The phylogenetic analysis showed that the KhFA and KhFB grouped with the newly denominated Xpp and Mpp (former ETX/Mtx) pesticidal protein groups, respectively. Altogether, this study has led to the discovery of two novel candidate pesticidal toxins in the lepidopteran toxic KhF strain.
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Effects of SpoIVA on the formation of spores and crystal protein in Bacillus thuringiensis. Microbiol Res 2020; 239:126523. [PMID: 32575022 DOI: 10.1016/j.micres.2020.126523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 11/20/2022]
Abstract
In addition to forming spores, Bacillus thuringiensis (Bt) 4.0718 can produce toxins, insecticidal crystal protein (ICP) and vegetative insecticidal protein (Vip). The Bt spoIVA was successfully knocked out by gene recombination and was shown to inhibit sporulation. The mutant strain also exhibited significantly decreased growth and crystal formation, which inhibited spore formation and partially reduced the rate of crystal synthesis. The 50 % lethal concentrations (LC50) values of Bt 4.0718, replacement, complementation and multi-copy mutant strains against the fourth larval stage of H. armigera was determined as 5.422, 6.776, 6.223 and 5.018 μg/mL, respectively. A total of 1814 proteins were identified through isobaric tags for relative and absolute protein (iTRAQ), with 41 and 54 up and downregulated proteins observed. Gene ontology enrichment analysis showed that differentially expressed proteins were primarily involved in the biological process and molecular function. Quantitative real-time PCR analysis confirmed that 9 differential expressed genes exhibited a positive correlation between changes at transcriptional and translational levels. The results of this study provide a basis for further studies of the metabolic regulatory network of spores and crystal protein formation. Moreover, they can be used to ecologically safe insecticide of farmland production because the constructed Bt spoIVA mutants did not produce spores.Provides new ideas for the targeted improvement and application of environmentally friendly spore-free strains.
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Alves GB, Melo FL, Oliveira EE, Haddi K, Costa LTM, Dias ML, Campos FS, Pereira EJG, Corrêa RFT, Ascêncio SD, Santos GR, Smagghe G, Ribeiro BM, Aguiar RWS. Comparative genomic analysis and mosquito larvicidal activity of four Bacillus thuringiensis serovar israelensis strains. Sci Rep 2020; 10:5518. [PMID: 32218451 PMCID: PMC7099026 DOI: 10.1038/s41598-020-60670-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
Bacillus thuringiensis serovar israelensis (Bti) is used to control insect vectors of human and animal diseases. In the present study, the toxicity of four strains of Bti, named T0124, T0131, T0137, and T0139, toward Aedes aegypti and Culex quinquefasciatus larvae was analyzed. The T0131 strain showed the highest larvicidal activity against A. aegypti (LC50 = 0.015 µg/ml) and C. quinquefasciatus larvae (LC50 = 0.035 µg/ml) when compared to the other strains. Furthermore, the genomic sequences of the four strains were obtained and compared. These Bti strains had chromosomes sizes of approximately 5.4 Mb with GC contents of ~35% and 5472–5477 putative coding regions. Three small plasmids (5.4, 6.8, and 7.6 kb) and three large plasmids (127, 235, and 359 kb) were found in the extrachromosomal content of all four strains. The SNP-based phylogeny revealed close relationship among isolates from this study and other Bti isolates, and SNPs analysis of the plasmids 127 kb did not reveal any mutations in δ-endotoxins genes. This newly acquired sequence data for these Bti strains may be useful in the search for novel insecticidal toxins to improve existing ones or develop new strategies for the biological control of important insect vectors of human and animal diseases.
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Affiliation(s)
- Giselly B Alves
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Fernando L Melo
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Eugenio E Oliveira
- Departmento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Khalid Haddi
- Departamento de Entomologia, Universidade Federal de Lavras, Lavras, MG, 37200-900, Brazil
| | - Lara T M Costa
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Marcelo L Dias
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Fabrício S Campos
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Eliseu J G Pereira
- Departmento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Roberto F T Corrêa
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Sergio D Ascêncio
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal (Rede Bionorte), Universidade Federal do Tocantins, Palmas, TO, 77413-070, Brazil
| | - Gil R Santos
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil
| | - Guy Smagghe
- Department of Plants and Crops, Ghent University, 9000, Ghent, Belgium
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Raimundo W S Aguiar
- Departamento de Biotecnologia, Universidade Federal de Tocantins, Gurupi, TO, 77413-070, Brazil.
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Fayad N, Patiño-Navarrete R, Kambris Z, Antoun M, Osta M, Chopineau J, Mahillon J, El Chamy L, Sanchis V, Kallassy Awad M. Characterization and Whole Genome Sequencing of AR23, a Highly Toxic Bacillus thuringiensis Strain Isolated from Lebanese Soil. Curr Microbiol 2019; 76:1503-1511. [PMID: 31563972 DOI: 10.1007/s00284-019-01775-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/21/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
The demand for sustainable and eco-friendly control methods of pests and insects is increasing worldwide. From this came the interest in Bacillus thuringiensis, an entomopathogenic bacterium capable of replacing chemical pesticides. However, the possibility of pests developing resistance to a particular strain may impair its use, and there is a need to identify novel strains of this species as potential commercial biopesticides. B. thuringiensis sv. israelensis is one of the most successful serovars, widely commercialized for its activity against black fly and mosquito larvae. In this study, we isolated, characterized, and sequenced a new Lebanese B. thuringiensis sv. israelensis isolate, strain AR23. Compared to the commercialized reference strain AM65-52 (Vectobac®, Sumitomo), AR23 showed an increased activity against several mosquito species. The genomic analysis revealed that this strain, compared to AM65-52, possesses a simplified plasmid content and an additional functional cry4Ba coding gene that most likely accounts for the increased effectiveness of this strain in mosquito larvae killing.
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Affiliation(s)
- Nancy Fayad
- Laboratory of Biodiversity and Functional Genomics, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rafael Patiño-Navarrete
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Zakaria Kambris
- Biology Department, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Mandy Antoun
- Laboratory of Biodiversity and Functional Genomics, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Institut Charles Gerhardt de Montpellier (ICGM), CNRS UMR 5253/UM/ENSCM Université de Montpellier Campus Triolet, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
- Université de Nîmes, Rue Georges Salan, 30000, Nîmes, France
| | - Mike Osta
- Biology Department, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Joel Chopineau
- Institut Charles Gerhardt de Montpellier (ICGM), CNRS UMR 5253/UM/ENSCM Université de Montpellier Campus Triolet, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
- Université de Nîmes, Rue Georges Salan, 30000, Nîmes, France
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laure El Chamy
- Génétique de La Drosophile Et Virulence Microbienne (GDVM), Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Vincent Sanchis
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Mireille Kallassy Awad
- Laboratory of Biodiversity and Functional Genomics, Faculty of Science, Université Saint-Joseph de Beyrouth, Beirut, Lebanon.
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Malovichko YV, Nizhnikov AA, Antonets KS. Repertoire of the Bacillus thuringiensis Virulence Factors Unrelated to Major Classes of Protein Toxins and Its Role in Specificity of Host-Pathogen Interactions. Toxins (Basel) 2019; 11:E347. [PMID: 31212976 PMCID: PMC6628457 DOI: 10.3390/toxins11060347] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/21/2019] [Accepted: 06/10/2019] [Indexed: 12/28/2022] Open
Abstract
Bacillus thuringiensis (Bt) is a Gram-positive soil bacteria that infects invertebrates, predominantly of Arthropoda phylum. Due to its immense host range Bt has become a leading producer of biopesticides applied both in biotechnology and agriculture. Cytotoxic effect of Bt, as well as its host specificity, are commonly attributed either to proteinaceous crystal parasporal toxins (Cry and Cyt) produced by bacteria in a stationary phase or to soluble toxins of Vip and Sip families secreted by vegetative cells. At the same time, numerous non-toxin virulence factors of Bt have been discovered, including metalloproteases, chitinases, aminopolyol antibiotics and nucleotide-mimicking moieties. These agents act at each stage of the B. thuringiensis invasion and contribute to cytotoxic properties of Bt strains enhancing toxin activity, ensuring host immune response evasion and participating in extracellular matrix degeneration. In this review we attempt to classify Bt virulence factors unrelated to major groups of protein toxins and discuss their putative role in the establishment of Bt specificity to various groups of insects.
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Affiliation(s)
- Yury V Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg 196608, Russia.
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Anton A Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg 196608, Russia.
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Kirill S Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg 196608, Russia.
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
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Cui Y, Märtlbauer E, Dietrich R, Luo H, Ding S, Zhu K. Multifaceted toxin profile, an approach toward a better understanding of probiotic Bacillus cereus. Crit Rev Toxicol 2019; 49:342-356. [PMID: 31116061 DOI: 10.1080/10408444.2019.1609410] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Strains of the Bacillus cereus group have been widely used as probiotics for human beings, food animals, plants, and environmental remediation. Paradoxically, B. cereus is responsible for both gastrointestinal and nongastrointestinal syndromes and represents an important opportunistic food-borne pathogen. Toxicity assessment is a fundamental issue to evaluate safety of probiotics. Here, we summarize the state of our current knowledge about the toxins of B. cereus sensu lato to be considered for safety assessment of probiotic candidates. Surfactin-like emetic toxin (cereulide) and various enterotoxins including nonhemolytic enterotoxin, hemolysin BL, and cytotoxin K are responsible for food poisoning outbreaks characterized by emesis and diarrhea. In addition, other factors, such as hemolysin II, Certhrax, immune inhibitor A1, and sphingomyelinase, contribute to toxicity and overall virulence of B. cereus.
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Affiliation(s)
- Yifang Cui
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , Beijing , China.,State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University , Beijing , China
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Ludwig-Maximilians-University Munich , Oberschleißheim , Germany
| | - Richard Dietrich
- Department of Veterinary Sciences, Ludwig-Maximilians-University Munich , Oberschleißheim , Germany
| | - Hailing Luo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University , Beijing , China
| | - Shuangyang Ding
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University , Beijing , China
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , Beijing , China.,National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University , Beijing , China
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11
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Chelliah R, Wei S, Park BJ, Park JH, Park YS, Kim SH, Jin YG, Oh DH. New perspectives on Mega plasmid sequence (poh1) in Bacillus thuringiensis ATCC 10792 harbouring antimicrobial, insecticidal and antibiotic resistance genes. Microb Pathog 2018; 126:14-18. [PMID: 30326263 DOI: 10.1016/j.micpath.2018.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/23/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Abstract
Bacillus thuringiensis promotes the growth of numerous economically important crops. The present study presents the complete genome sequence for a mega plasmid present in the type strain of B. thuringiensis ATCC 10792, a typical spore-forming Gram-positive bacterium with insecticidal activity, and investigates its genetic characteristics. The genome was sequenced and assembled de novo using Pac-Bio sequencers and the Hierarchical Genome Assembly Process, respectively. Further genome annotation was performed, and a total of 489 proteins and a novel mega-plasmid (poh1) with 584,623 bps were identified. The organization of poh1 revealed the genes involved in the insecticidal toxin pathway. The genes responsible for antimicrobial, insecticidal and antibiotic activities were well conserved in poh1, indicating an intimate association with plant hosts. The poh1 plasmid contains the gene encoding a novel crystal protein kinase responsible for production of zeta toxin, which poisons insects and other Gram-negative bacteria through the global inhibition of peptidoglycan synthesis. Lantibiotics are a group of bacteriocins that include the biologically active antimicrobial peptide Paenibacillin. Further, poh1 also contains the genes that encode the gramicidin S prototypical antibiotic peptide and tetracycline resistance protein. In conclusion, the strain-specific genes of B. thuringiensis strain ATCC 10792 were identified through complete genome sequencing and bioinformatics data based on major pathogenic factors that contribute to further studies of the pathogenic mechanism and phenotype analyses.
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Affiliation(s)
- Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Shuai Wei
- Department of Medical Biomaterials Engineering and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Republic of Korea
| | - Byung-Jae Park
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Joong-Hyun Park
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Youn-Seo Park
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Se-Hun Kim
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea
| | - Yong-Guo Jin
- National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, 24341, Republic of Korea.
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Daas MS, Rosana ARR, Acedo JZ, Douzane M, Nateche F, Kebbouche-Gana S, Vederas JC. Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough. Stand Genomic Sci 2018; 13:25. [PMID: 30344888 PMCID: PMC6186030 DOI: 10.1186/s40793-018-0331-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form parasporal crystals containing proteinaceous toxins. It is a member of the Bacillus cereus sensu lato, a group with low genetic diversity but produces several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of B. thuringiensis DNG9. The genome encodes several gene inventories for the biosynthesis of bioactive compounds such as zwittermycin A, petrobactin, insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins. We expect the genome information of strain DNG9 will provide another model system to study pathogenicity against insect pests, plant diseases, and antimicrobial compound mining and comparative phylogenesis among the Bacillus cereus sensu lato group.
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Affiliation(s)
- Mohamed Seghir Daas
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | | | - Jeella Z. Acedo
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
| | - Malika Douzane
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | - Farida Nateche
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology–Houari Boumediene, 16111, Bab Ezzouar, Algiers, Algeria
| | - Salima Kebbouche-Gana
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
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Zheng D, Zeng Z, Xue B, Deng Y, Sun M, Tang YJ, Ruan L. Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes. Microbiol Res 2018; 215:22-28. [DOI: 10.1016/j.micres.2018.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/23/2018] [Accepted: 06/02/2018] [Indexed: 11/28/2022]
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BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43. ACTA BIOMEDICA SCIENTIFICA 2018. [DOI: 10.29413/abs.2018-3.5.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background. CRISPR/Cas systems loci are one of the functionally important patterns in bacterial genome which perform the role of “adaptive immune defense” from foreign nucleic acids. The study of CRISPR/Cas systems structure in genomes of plasmids and phages provide new information about the evolution of this systems in bacterial hosts.Aims. A search of CRISPR/Cas systems structures in pCT281 plasmid from Bacillus thuringiensis subsp. chinensis strain CT-43 using bioinformatic methods.Materials and methods. Search studies using bioinformatics methods were performed with the genome of pCT281 plasmid of B. thuringiensis subsp. chinensis strain CT-43 from the RefSeq database. To search for the CRISPR/Cas system structure MacSyFinder (ver. 1.0.5) and three combined algorithms were used: CRISPRFinder; PILER-CR; CRISPR Recognition Tool (CRT). The consensus repeat sequence was generated in WebLogo 3.Results and discussion. In pCT281 plasmid we detected one locus of CRISPR/Cas system of the type I-C which contains 2 CRISPR-cassettes and 4 cas-genes located between them. The CRISPR-cassette 1 includes 10 spacers from 32 to 35 bp and 11 repeats 32bp in length. 5 spacers (33–35 bp) separated by 6 repeats 32 bp in length were detected in the CRISPR-cassette 2.Conclusions. The bioinformatic methods used in this study enable to conduct a search of CRISPR/Cas systems structures in plasmid genomes. The presence of the CRISPR-Cas locus in pCT281 plasmid confirms a possible transfer of this system from the nucleoid to this plasmid. The detected spacers provide information about phages this bacteria was encountered.
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Fiedoruk K, Daniluk T, Mahillon J, Leszczynska K, Swiecicka I. Genetic Environment of cry1 Genes Indicates Their Common Origin. Genome Biol Evol 2018; 9:2265-2275. [PMID: 29617829 PMCID: PMC5604178 DOI: 10.1093/gbe/evx165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/21/2022] Open
Abstract
Although in Bacillus thuringiensis the cry genes coding for the insecticidal crystal proteins are plasmid-borne and are usually associated with mobile genetic elements, several aspects related to their genomic organization, diversification, and transmission remain to be elucidated. Plasmids of B. thuringiensis and other members of the Bacillus cereus group (n = 364) deposited in GenBank were screened for the presence of cry1 genes, and their genetic environment was analyzed using a comparative bioinformatic approach. The cry1 genes were identified in 27 B. thuringiensis plasmids ranging from 64 to 761 kb, and were predominantly associated with the ori44, ori60, or double orf156/orf157 and pXO1-16/pXO1-14 replication systems. In general, the cry1 genes occur individually or as a part of an insecticidal pathogenicity island (PAI), and are preceded by genes coding for an N-acetylmuramoyl-l-alanine amidase and a putative K+(Na+)/H+ antiporter. However, except in the case of the PAI, the latter gene is disrupted by the insertion of IS231B. Similarly, numerous mobile elements were recognized in the region downstream of cry1, except for cry1I that follows cry1A in the PAI. Therefore, the cassette involving cry1 and these two genes, flanked by transposable elements, named as the cry1 cassette, was the smallest cry1-carrying genetic unit recognized in the plasmids. Conservation of the genomic environment of the cry1 genes carried by various plasmids strongly suggests a common origin, possibly from an insecticidal PAI carried by B. thuringiensis megaplasmids.
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Affiliation(s)
- Krzysztof Fiedoruk
- Department of Microbiology, Medical University of Bialystok, Poland
- Corresponding author: E-mail:
| | - Tamara Daniluk
- Department of Microbiology, Medical University of Bialystok, Poland
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Izabela Swiecicka
- Department of Microbiology, University of Bialystok, Poland
- Laboratory of Applied Microbiology, University of Bialystok, Poland
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16
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Yik LY, Chin GJWL, Budiman C, Joseph CG, Musta B, Rodrigues KF. Adaptive Strategies of Bacillus thuringiensis Isolated from Acid Mine Drainage Site in Sabah, Malaysia. Indian J Microbiol 2018; 58:165-173. [PMID: 29651175 DOI: 10.1007/s12088-017-0701-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/26/2017] [Indexed: 11/29/2022] Open
Abstract
The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage.
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Affiliation(s)
- Low Yi Yik
- 1Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | | | - Cahyo Budiman
- 1Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Collin Glenn Joseph
- 2Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Baba Musta
- 2Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
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Fu Y, Yu Z, Liu S, Chen B, Zhu L, Li Z, Chou SH, He J. c-di-GMP Regulates Various Phenotypes and Insecticidal Activity of Gram-Positive Bacillus thuringiensis. Front Microbiol 2018; 9:45. [PMID: 29487570 PMCID: PMC5816809 DOI: 10.3389/fmicb.2018.00045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/09/2018] [Indexed: 12/26/2022] Open
Abstract
C-di-GMP has been well investigated to play significant roles in the physiology of many Gram-negative bacteria. However, its effect on Gram-positive bacteria is less known. In order to more understand the c-di-GMP functions in Gram-positive bacteria, we have carried out a detailed study on the c-di-GMP-metabolizing enzymes and their physiological functions in Bacillus thuringiensis, a Gram-positive entomopathogenic bacterium that has been applied as an insecticide successfully. We performed a systematic study on the ten putative c-di-GMP-synthesizing enzyme diguanylate cyclases (DGCs) and c-di-GMP-degrading enzyme phosphodiesterases (PDEs) in B. thuringiensis BMB171, and artificially elevated the intracellular c-di-GMP level in BMB171 by deleting one or more pde genes. We found increasing level of intracellular c-di-GMP exhibits similar activities as those in Gram-negative bacteria, including altered activities in cell motility, biofilm formation, and cell-cell aggregation. Unexpectedly, we additionally found a novel function exhibited by the increasing level of c-di-GMP to promote the insecticidal activity of this bacterium against Helicoverpa armigera. Through whole-genome transcriptome profile analyses, we found that 4.3% of the B. thuringiensis genes were differentially transcribed when c-di-GMP level was increased, and 77.3% of such gene products are involved in some regulatory pathways not reported in other bacteria to date. In summary, our study represents the first comprehensive report on the c-di-GMP-metabolizing enzymes, their effects on phenotypes, and the transcriptome mediated by c-di-GMP in an important Gram-positive bacterium.
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Affiliation(s)
- Yang Fu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhaoqing Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shu Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhou Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- NCHU Agricultural Biotechnology Center, Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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18
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Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC. The microbiomes of blowflies and houseflies as bacterial transmission reservoirs. Sci Rep 2017; 7:16324. [PMID: 29176730 PMCID: PMC5701178 DOI: 10.1038/s41598-017-16353-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/10/2017] [Indexed: 12/25/2022] Open
Abstract
Blowflies and houseflies are mechanical vectors inhabiting synanthropic environments around the world. They feed and breed in fecal and decaying organic matter, but the microbiome they harbour and transport is largely uncharacterized. We sampled 116 individual houseflies and blowflies from varying habitats on three continents and subjected them to high-coverage, whole-genome shotgun sequencing. This allowed for genomic and metagenomic analyses of the host-associated microbiome at the species level. Both fly host species segregate based on principal coordinate analysis of their microbial communities, but they also show an overlapping core microbiome. Legs and wings displayed the largest microbial diversity and were shown to be an important route for microbial dispersion. The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.
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Affiliation(s)
- Ana Carolina M Junqueira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Enzo Acerbi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Balakrishnan N V Premkrishnan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Paul I Costea
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Bodo Linz
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, 30602, GA, USA
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Daniel F Paulo
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Nicolas E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Nur A Hasan
- CosmosID Inc, Rockville, MD, 20850, USA
- Center for Bioinformatics and Computational Biology, University of Maryland. Institute for Computational Biology, University of Maryland College Park, College Park, MD, 20742, USA
| | - Rita R Colwell
- CosmosID Inc, Rockville, MD, 20850, USA
- Center for Bioinformatics and Computational Biology, University of Maryland. Institute for Computational Biology, University of Maryland College Park, College Park, MD, 20742, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Ana Maria L Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Donald A Bryant
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
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Comparative Genomics of Bacillus thuringiensis Reveals a Path to Specialized Exploitation of Multiple Invertebrate Hosts. mBio 2017; 8:mBio.00822-17. [PMID: 28790205 PMCID: PMC5550751 DOI: 10.1128/mbio.00822-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the genetic basis of host shifts is a key genomic question for pathogen and parasite biology. The Bacillus cereus group, which encompasses Bacillus thuringiensis and Bacillus anthracis, contains pathogens that can infect insects, nematodes, and vertebrates. Since the target range of the essential virulence factors (Cry toxins) and many isolates is well known, this group presents a powerful system for investigating how pathogens can diversify and adapt to phylogenetically distant hosts. Specialization to exploit insects occurs at the level of the major clade and is associated with substantial changes in the core genome, and host switching between insect orders has occurred repeatedly within subclades. The transfer of plasmids with linked cry genes may account for much of the adaptation to particular insect orders, and network analysis implies that host specialization has produced strong associations between key toxin genes with similar targets. Analysis of the distribution of plasmid minireplicons shows that plasmids with orf156 and orf157, which carry genes encoding toxins against Lepidoptera or Diptera, were contained only by B. thuringiensis in the specialized insect clade (clade 2), indicating that tight genome/plasmid associations have been important in adaptation to invertebrate hosts. Moreover, the accumulation of multiple virulence factors on transposable elements suggests that cotransfer of diverse virulence factors is advantageous in terms of expanding the insecticidal spectrum, overcoming insect resistance, or through gains in pathogenicity via synergistic interactions between toxins.IMPORTANCE Population genomics have provided many new insights into the formation, evolution, and dynamics of bacterial pathogens of humans and other higher animals, but these pathogens usually have very narrow host ranges. As a pathogen of insects and nematodes, Bacillus thuringiensis, which produces toxins showing toxicity to many orders of insects and other invertebrates, can be used as a model to study the evolution of pathogens with wide host ranges. Phylogenomic analysis revealed that host specialization and switching occur at the level of the major clade and subclade, respectively. A toxin gene co-occurrence network indicates that multiple toxins with similar targets were accumulated by the same cell in the whole species. This accumulation may be one of the strategies that B. thuringiensis has used to fight against host resistance. This kind of formation and evolution of pathogens represents a different path used against multiple invertebrate hosts from that used against higher animals.
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Sauka DH, Benintende GB. Diversity and distribution of lepidopteran-specific toxin genes in Bacillus thuringiensis strains from Argentina. Rev Argent Microbiol 2017; 49:273-281. [PMID: 28576334 DOI: 10.1016/j.ram.2017.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 02/01/2017] [Accepted: 02/24/2017] [Indexed: 11/29/2022] Open
Abstract
A total of 268 Bacillus thuringiensis strains obtained from different sources of Argentina were analyzed to determine the diversity and distribution of the cry1, cry2, cry8, cry9 and vip3A genes encoding for lepidopteran-specific insecticidal proteins. Twin strains were excluded. Ten different profiles were detected among the 80 selected B. thuringiensis strains. Two of these profiles (cry1Aa, cry1Ac, cry1Ia, cry2Aa, cry2Ab and vip3Aa (35/80), and cry1Aa, cry1Ab, cry1Ac, cry1Ia, cry2Aa, cry2Ab and vip3Aa (25/80)) pooled 75% of the strains. The existence of this low diversity is rare, since in most of the studied collections a great diversity of insecticidal toxin gene profiles has been described. In addition, the most frequently detected profile was also most frequently derived from soil (70%), stored product dust (59%) and spider webs (50%). In contrast, the cry1Aa, cry1Ab, cry1Ac, cry1Ia, cry2Aa, cry2Ab and vip3Aa profiles were mainly detected in strains isolated from leaves (40%) and dead insect larvae (50%). Six of the identified insecticidal toxin gene profiles were discovered in strains isolated from stored product dust and leaves indicating higher diversity of profiles in these kinds of sources than in others. Some strains with high insecticidal activity against Epinotia aporema (Lepidoptera) larvae were identified, which is important to explore future microbial strategies for the control of this crop pest in the region.
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Affiliation(s)
- Diego H Sauka
- Instituto de Microbiología y Zoología Agrícola INTA, CC No 25 (1712), Castelar, Buenos Aires, Argentina.
| | - Graciela B Benintende
- Instituto de Microbiología y Zoología Agrícola INTA, CC No 25 (1712), Castelar, Buenos Aires, Argentina
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Djenane Z, Nateche F, Amziane M, Gomis-Cebolla J, El-Aichar F, Khorf H, Ferré J. Assessment of the Antimicrobial Activity and the Entomocidal Potential of Bacillus thuringiensis Isolates from Algeria. Toxins (Basel) 2017; 9:E139. [PMID: 28406460 PMCID: PMC5408213 DOI: 10.3390/toxins9040139] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 03/29/2017] [Accepted: 04/11/2017] [Indexed: 11/23/2022] Open
Abstract
This work represents the first initiative to analyze the distribution of B. thuringiensis in Algeria and to evaluate the biological potential of the isolates. A total of 157 isolates were recovered, with at least one isolate in 94.4% of the samples. The highest Bt index was found in samples from rhizospheric soil (0.48) and from the Mediterranean area (0.44). Most isolates showed antifungal activity (98.5%), in contrast to the few that had antibacterial activity (29.9%). A high genetic diversity was made evident by the finding of many different crystal shapes and various combinations of shapes within a single isolate (in 58.4% of the isolates). Also, over 50% of the isolates harbored cry1, cry2, or cry9 genes, and 69.3% contained a vip3 gene. A good correlation between the presence of chitinase genes and antifungal activity was observed. More than half of the isolates with a broad spectrum of antifungal activity harbored both endochitinase and exochitinase genes. Interestingly, 15 isolates contained the two chitinase genes and all of the above cry family genes, with some of them harboring a vip3 gene as well. The combination of this large number of genes coding for entomopathogenic proteins suggests a putative wide range of entomotoxic activity.
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Affiliation(s)
- Zahia Djenane
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32, EL ALIA, Bab Ezzouar, 16111 Algiers, Algeria.
- ERI BIOTECMED and Department of Genetics, Universitat de València, Dr. Moliner, 50, BURJASSOT, 46100 Valencia, Spain.
- Department of Science and Technology, Faculty of Science, University Dr Yahia Frès, 26000 Médéa, Algeria.
| | - Farida Nateche
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32, EL ALIA, Bab Ezzouar, 16111 Algiers, Algeria.
| | - Meriam Amziane
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32, EL ALIA, Bab Ezzouar, 16111 Algiers, Algeria.
| | - Joaquín Gomis-Cebolla
- ERI BIOTECMED and Department of Genetics, Universitat de València, Dr. Moliner, 50, BURJASSOT, 46100 Valencia, Spain.
| | - Fairouz El-Aichar
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32, EL ALIA, Bab Ezzouar, 16111 Algiers, Algeria.
| | - Hassiba Khorf
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32, EL ALIA, Bab Ezzouar, 16111 Algiers, Algeria.
| | - Juan Ferré
- ERI BIOTECMED and Department of Genetics, Universitat de València, Dr. Moliner, 50, BURJASSOT, 46100 Valencia, Spain.
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Bacillus thuringiensis: a successful insecticide with new environmental features and tidings. Appl Microbiol Biotechnol 2017; 101:2691-2711. [PMID: 28235989 DOI: 10.1007/s00253-017-8175-y] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/31/2017] [Accepted: 02/02/2017] [Indexed: 12/15/2022]
Abstract
Bacillus thuringiensis (Bt) is known as the most successful microbial insecticide against different orders of insect pests in agriculture and medicine. Moreover, Bt toxin genes also have been efficiently used to enhance resistance to insect pests in genetically modified crops. In light of the scientific advantages of new molecular biology technologies, recently, some other new potentials of Bt have been explored. These new environmental features include the toxicity against nematodes, mites, and ticks, antagonistic effects against plant and animal pathogenic bacteria and fungi, plant growth-promoting activities (PGPR), bioremediation of different heavy metals and other pollutants, biosynthesis of metal nanoparticles, production of polyhydroxyalkanoate biopolymer, and anticancer activities (due to parasporins). This review comprehensively describes recent advances in the Bt whole-genome studies, the last updated known Bt toxins and their functions, and application of cry genes in plant genetic engineering. Moreover, the review thoroughly describes the new features of Bt which make it a suitable cell factory that might be used for production of different novel valuable bioproducts.
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Navas LE, Amadio AF, Ortiz EM, Sauka DH, Benintende GB, Berretta MF, Zandomeni RO. Complete Sequence and Organization of pFR260, the Bacillus thuringiensis INTA Fr7-4 Plasmid Harboring Insecticidal Genes. J Mol Microbiol Biotechnol 2017; 27:43-54. [DOI: 10.1159/000451056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/23/2016] [Indexed: 11/19/2022] Open
Abstract
We report the complete sequence and analysis of pFR260, a novel megaplasmid of 260,595 bp from the <i>Bacillus thuringiensis</i> strain INTA Fr7-4 isolated in Argentina. It carries 7 insecticidal genes: 3 <i>cry8</i> copies previously reported, 2 <i>vip1,</i> and 2 <i>vip2</i>. Also, it carries a gene encoding a putative atypical Cry protein. These genes are arranged in a region of approximately 105 kbp in size with characteristics of a pathogenicity island with a potential coleopteran-specific insecticide profile. DNA strand composition asymmetry, as determined by GC skew analysis, and the presence of a Rep protein involved in the initiation of replication suggest a bidirectional <i>theta</i> mechanism of replication. In addition, many genes involved in conjugation and a CRISPR-Cas system were detected. The pFR260 sequence was deposited in GenBank under accession number KX258624.
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Du C, Cao S, Shi X, Nie X, Zheng J, Deng Y, Ruan L, Peng D, Sun M. Genetic and Biochemical Characterization of a Gene Operon for trans-Aconitic Acid, a Novel Nematicide from Bacillus thuringiensis. J Biol Chem 2017; 292:3517-3530. [PMID: 28087696 DOI: 10.1074/jbc.m116.762666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/31/2016] [Indexed: 12/31/2022] Open
Abstract
trans-Aconitic acid (TAA) is an isomer of cis-aconitic acid (CAA), an intermediate of the tricarboxylic acid cycle that is synthesized by aconitase. Although TAA production has been detected in bacteria and plants for many years and is known to be a potent inhibitor of aconitase, its biosynthetic origins and the physiological relevance of its activity have remained unclear. We have serendipitously uncovered key information relevant to both of these questions. Specifically, in a search for novel nematicidal factors from Bacillus thuringiensis, a significant nematode pathogen harboring many protein virulence factors, we discovered a high yielding component that showed activity against the plant-parasitic nematode Meloidogyne incognita and surprisingly identified it as TAA. Comparison with CAA, which displayed a much weaker nematicidal effect, suggested that TAA is specifically synthesized by B. thuringiensis as a virulence factor. Analysis of mutants deficient in plasmids that were anticipated to encode virulence factors allowed us to isolate a TAA biosynthesis-related (tbr) operon consisting of two genes, tbrA and tbrB We expressed the corresponding proteins, TbrA and TbrB, and characterized them as an aconitate isomerase and TAA transporter, respectively. Bioinformatics analysis of the TAA biosynthetic gene cluster revealed the association of the TAA genes with transposable elements relevant for horizontal gene transfer as well as a distribution across B. cereus bacteria and other B. thuringiensis strains, suggesting a general role for TAA in the interactions of B. cereus group bacteria with nematode hosts in the soil environment. This study reveals new bioactivity for TAA and the TAA biosynthetic pathway, improving our understanding of virulence factors employed by B. thuringiensis pathogenesis and providing potential implications for nematode management applications.
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Affiliation(s)
- Cuiying Du
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiyun Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Shi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangtao Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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Wang P, Zhu Y, Zhang Y, Zhang C, Xu J, Deng Y, Peng D, Ruan L, Sun M. Mob/oriT, a mobilizable site-specific recombination system for unmarked genetic manipulation in Bacillus thuringiensis and Bacillus cereus. Microb Cell Fact 2016; 15:108. [PMID: 27286821 PMCID: PMC4902927 DOI: 10.1186/s12934-016-0492-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/23/2016] [Indexed: 11/29/2022] Open
Abstract
Background Bacillus thuringiensis and Bacillus cereus are two important species in B. cereus group. The intensive study of these strains at the molecular level and construction of genetically modified bacteria requires the development of efficient genetic tools. To insert genes into or delete genes from bacterial chromosomes, marker-less manipulation methods were employed. Results We present a novel genetic manipulation method for B. thuringiensis and B. cereus strains that does not leave selection markers. Our approach takes advantage of the relaxase Mob02281 encoded by plasmid pBMB0228 from Bacillus thuringiensis. In addition to its mobilization function, this Mob protein can mediate recombination between oriT sites. The Mob02281 mobilization module was associated with a spectinomycin-resistance gene to form a Mob-Spc cassette, which was flanked by the core 24-bp oriT sequences from pBMB0228. A strain in which the wild-type chromosome was replaced with the modified copy containing the Mob-Spc cassette at the target locus was obtained via homologous recombination. Thus, the spectinomycin-resistance gene can be used to screen for Mob-Spc cassette integration mutants. Recombination between the two oriT sequences mediated by Mob02281, encoded by the Mob-Spc cassette, resulted in the excision of the Mob-Spc cassette, producing the desired chromosomal alteration without introducing unwanted selection markers. We used this system to generate an in-frame deletion of a target gene in B. thuringiensis as well as a gene located in an operon of B. cereus. Moreover, we demonstrated that this system can be used to introduce a single gene or an expression cassette of interest in B. thuringiensis. Conclusion The Mob/oriT recombination system provides an efficient method for unmarked genetic manipulation and for constructing genetically modified bacteria of B. thuringiensis and B. cereus. Our method extends the available genetic tools for B. thuringiensis and B. cereus strains. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0492-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengxia Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yiguang Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuyang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chunyi Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianyi Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
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Manga P, Klingeman DM, Lu TYS, Mehlhorn TL, Pelletier DA, Hauser LJ, Wilson CM, Brown SD. Replicates, Read Numbers, and Other Important Experimental Design Considerations for Microbial RNA-seq Identified Using Bacillus thuringiensis Datasets. Front Microbiol 2016; 7:794. [PMID: 27303383 PMCID: PMC4886094 DOI: 10.3389/fmicb.2016.00794] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
RNA-seq is being used increasingly for gene expression studies and it is revolutionizing the fields of genomics and transcriptomics. However, the field of RNA-seq analysis is still evolving. Therefore, we specifically designed this study to contain large numbers of reads and four biological replicates per condition so we could alter these parameters and assess their impact on differential expression results. Bacillus thuringiensis strains ATCC10792 and CT43 were grown in two Luria broth medium lots on four dates and transcriptomics data were generated using one lane of sequence output from an Illumina HiSeq2000 instrument for each of the 32 samples, which were then analyzed using DESeq2. Genome coverages across samples ranged from 87 to 465X with medium lots and culture dates identified as major variation sources. Significantly differentially expressed genes (5% FDR, two-fold change) were detected for cultures grown using different medium lots and between different dates. The highly differentially expressed iron acquisition and metabolism genes, were a likely consequence of differing amounts of iron in the two media lots. Indeed, in this study RNA-seq was a tool for predictive biology since we hypothesized and confirmed the two LB medium lots had different iron contents (~two-fold difference). This study shows that the noise in data can be controlled and minimized with appropriate experimental design and by having the appropriate number of replicates and reads for the system being studied. We outline parameters for an efficient and cost effective microbial transcriptomics study.
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Affiliation(s)
- Punita Manga
- Graduate School of Genome Science and Technology, University of TennesseeKnoxville, TN, USA; BioEnergy Science Center, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Dawn M Klingeman
- BioEnergy Science Center, Oak Ridge National LaboratoryOak Ridge, TN, USA; Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Tonia L Mehlhorn
- Environmental Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dale A Pelletier
- Graduate School of Genome Science and Technology, University of TennesseeKnoxville, TN, USA; Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Loren J Hauser
- Graduate School of Genome Science and Technology, University of TennesseeKnoxville, TN, USA; Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Charlotte M Wilson
- BioEnergy Science Center, Oak Ridge National LaboratoryOak Ridge, TN, USA; Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Steven D Brown
- Graduate School of Genome Science and Technology, University of TennesseeKnoxville, TN, USA; BioEnergy Science Center, Oak Ridge National LaboratoryOak Ridge, TN, USA; Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
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27
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Zhou H, Zheng C, Su J, Chen B, Fu Y, Xie Y, Tang Q, Chou SH, He J. Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep 2016; 6:20871. [PMID: 26892868 PMCID: PMC4759541 DOI: 10.1038/srep20871] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/11/2016] [Indexed: 12/22/2022] Open
Abstract
c-di-GMP riboswitches are structured RNAs located in the 5'-untranslated regions (5'-UTRs) of mRNAs that regulate expression of downstream genes in response to changing concentrations of the second messenger c-di-GMP. We discovered three complete c-di-GMP riboswitches (Bc3, Bc4 and Bc5 RNA) with similar structures, which are arranged in tandem to constitute a triple-tandem (Bc3-5 RNA) riboswitch in the 5'-UTR of the cspABCDE mRNA in Bacillus thuringiensis subsp. chinensis CT-43. Our results showed that this natural triple-tandem riboswitch controlled the expression of the reporter gene more stringently and digitally than the double-tandem or single riboswitch. A sandwich-like dual-fluorescence reporter was further constructed by fusing the Bc3-5 RNA gene between the two fluorescence protein genes amcyan and turborfp. This reporter strain was found to exhibit detectable fluorescence color changes under bright field in response to intracellular c-di-GMP level altered by induced expression of diguanylate cyclase (DGC) PleD. Using this system, two putative membrane-bound DGCs from B. thuringiensis and Xanthomonas oryzae were verified to be functional by replacing pleD with the corresponding DGC genes. This report represented the first native triple-tandem riboswitch that was applied to serve as a riboswitch-based dual-fluorescence reporter for the efficient and convenient verification of putative DGC activity in vivo.
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Affiliation(s)
- Hang Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Cao Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Jianmei Su
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Bo Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Yang Fu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Yuqun Xie
- Key Laboratory of Fermentation Engineering (Ministry of Education), College of Bioengineering, Hubei University of Technology, Wuhan, Hubei 430068, People's Republic of China
| | - Qing Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Shan-Ho Chou
- Institute of Biochemistry, and NCHU Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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28
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Sánchez-Soto A, Saavedra-González G, Ibarra J, Salcedo-Hernández R, Barboza-Corona J, Del Rincón-Castro M. Detection of β-exotoxin synthesis in Bacillus thuringiensis
using an easy bioassay with the nematode Caenorhabditis elegans. Lett Appl Microbiol 2015; 61:562-7. [DOI: 10.1111/lam.12493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/23/2015] [Accepted: 09/08/2015] [Indexed: 12/14/2022]
Affiliation(s)
- A.I. Sánchez-Soto
- Departamento de Alimentos; División de Ciencias de la Vida; Universidad de Guanajuato; Irapuato México
| | - G.I. Saavedra-González
- Departamento de Alimentos; División de Ciencias de la Vida; Universidad de Guanajuato; Irapuato México
| | - J.E. Ibarra
- Departamento de Biotecnología y Bioquímica; CINVESTAV; Irapuato México
| | - R. Salcedo-Hernández
- Departamento de Alimentos; División de Ciencias de la Vida; Universidad de Guanajuato; Irapuato México
- Posgrado en Biociencias División de Ciencias de la Vida, Universidad de Guanajuato; Irapuato México
| | - J.E. Barboza-Corona
- Departamento de Alimentos; División de Ciencias de la Vida; Universidad de Guanajuato; Irapuato México
- Posgrado en Biociencias División de Ciencias de la Vida, Universidad de Guanajuato; Irapuato México
| | - M.C. Del Rincón-Castro
- Departamento de Alimentos; División de Ciencias de la Vida; Universidad de Guanajuato; Irapuato México
- Posgrado en Biociencias División de Ciencias de la Vida, Universidad de Guanajuato; Irapuato México
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29
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Genomic and transcriptomic insights into the efficient entomopathogenicity of Bacillus thuringiensis. Sci Rep 2015; 5:14129. [PMID: 26411888 PMCID: PMC4585936 DOI: 10.1038/srep14129] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/31/2015] [Indexed: 11/19/2022] Open
Abstract
Bacillus thuringiensis has been globally used as a microbial pesticide for over 70 years. However, information regarding its various adaptions and virulence factors and their roles in the entomopathogenic process remains limited. In this work, we present the complete genomes of two industrially patented Bacillus thuringiensis strains (HD-1 and YBT-1520). A comparative genomic analysis showed a larger and more complicated genome constitution that included novel insecticidal toxicity-related genes (ITRGs). All of the putative ITRGs were summarized according to the steps of infection. A comparative genomic analysis showed that highly toxic strains contained significantly more ITRGs, thereby providing additional strategies for infection, immune evasion, and cadaver utilization. Furthermore, a comparative transcriptomic analysis suggested that a high expression of these ITRGs was a key factor in efficient entomopathogenicity. We identified an active extra urease synthesis system in the highly toxic strains that may aid B. thuringiensis survival in insects (similar to previous results with well-known pathogens). Taken together, these results explain the efficient entomopathogenicity of B. thuringiensis. It provides novel insights into the strategies used by B. thuringiensis to resist and overcome host immune defenses and helps identify novel toxicity factors.
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Abstract
Fifty complete Bacillus genome sequences and associated plasmids were compared using the “feature frequency profile” (FFP) method. The resulting whole-genome phylogeny supports the placement of three Bacillus species (B. thuringiensis, B. anthracis and B. cereus) as a single clade. The monophyletic status of B. anthracis was strongly supported by the analysis. FFP proved to be more effective in inferring the phylogeny of Bacillus than methods based on single gene sequences [16s rRNA gene, GryB (gyrase subunit B) and AroE (shikimate-5-dehydrogenase)] analyses. The findings of FFP analysis were verified using kSNP v2 (alignment-free sequence analysis method) and Harvest suite (core genome sequence alignment method).
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31
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Complete Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Pasteur Institute Standard. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00710-15. [PMID: 26139717 PMCID: PMC4490846 DOI: 10.1128/genomea.00710-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genome sequence of Bacillus thuringiensis serovar tolworthi strain Pasteur Institute Standard was determined. The genome consists of a 5.9-Mb chromosome and eight plasmids, one of which is linear. The second largest plasmid (293 kb) carries the genes encoding insecticidal proteins.
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Rang J, He H, Wang T, Ding X, Zuo M, Quan M, Sun Y, Yu Z, Hu S, Xia L. Comparative analysis of genomics and proteomics in Bacillus thuringiensis 4.0718. PLoS One 2015; 10:e0119065. [PMID: 25781161 PMCID: PMC4363619 DOI: 10.1371/journal.pone.0119065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Bacillus thuringiensis is a widely used biopesticide that produced various insecticidal active substances during its life cycle. Separation and purification of numerous insecticide active substances have been difficult because of the relatively short half-life of such substances. On the other hand, substances can be synthetized at different times during development, so samples at different stages have to be studied, further complicating the analysis. A dual genomic and proteomic approach would enhance our ability to identify such substances, and particularily using mass spectrometry-based proteomic methods. The comparative analysis for genomic and proteomic data have showed that not all of the products deduced from the annotated genome could be identified among the proteomic data. For instance, genome annotation results showed that 39 coding sequences in the whole genome were related to insect pathogenicity, including five cry genes. However, Cry2Ab, Cry1Ia, Cytotoxin K, Bacteriocin, Exoenzyme C3 and Alveolysin could not be detected in the proteomic data obtained. The sporulation-related proteins were also compared analysis, results showed that the great majority sporulation-related proteins can be detected by mass spectrometry. This analysis revealed Spo0A~P, SigF, SigE(+), SigK(+) and SigG(+), all known to play an important role in the process of spore formation regulatory network, also were displayed in the proteomic data. Through the comparison of the two data sets, it was possible to infer that some genes were silenced or were expressed at very low levels. For instance, found that cry2Ab seems to lack a functional promoter while cry1Ia may not be expressed due to the presence of transposons. With this comparative study a relatively complete database can be constructed and used to transform hereditary material, thereby prompting the high expression of toxic proteins. A theoretical basis is provided for constructing highly virulent engineered bacteria and for promoting the application of proteogenomics in the life sciences.
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Affiliation(s)
- Jie Rang
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Hao He
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Ting Wang
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Xuezhi Ding
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
- * E-mail: (XZD); (LQX)
| | - Mingxing Zuo
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Meifang Quan
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Yunjun Sun
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Ziquan Yu
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Shengbiao Hu
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
| | - Liqiu Xia
- College of Life Science, Hunan Normal University, Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, Changsha, China
- * E-mail: (XZD); (LQX)
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33
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Zhu L, Tian LJ, Zheng J, Gao QL, Wang YY, Peng DH, Ruan LF, Sun M. Complete genome sequence of Bacillus thuringiensis serovar galleriae strain HD-29, a typical strain of commercial biopesticide. J Biotechnol 2015; 195:108-9. [DOI: 10.1016/j.jbiotec.2014.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
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34
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High-resolution melt analysis for rapid comparison of bacterial community compositions. Appl Environ Microbiol 2015; 80:3568-75. [PMID: 24610853 DOI: 10.1128/aem.03923-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition.
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35
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Zheng J, Guan Z, Cao S, Peng D, Ruan L, Jiang D, Sun M. Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group. BMC Genomics 2015; 16:6. [PMID: 25608745 PMCID: PMC4326196 DOI: 10.1186/s12864-014-1206-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 12/24/2014] [Indexed: 01/12/2023] Open
Abstract
Background Prokaryotic plasmids have played significant roles in the evolution of bacterial genomes and have a great impact on the metabolic functions of the host cell. Many bacterial strains contain multiple plasmids, but the relationships between bacterial plasmids and chromosomes are unclear. We focused on plasmids from the Bacillus cereus group because most strains contain several plasmids. Results We collected the genome sequences of 104 plasmids and 20 chromosomes from B. cereus group strains, and we studied the relationships between plasmids and chromosomes by focusing on the pan-genomes of these plasmids and chromosomes. In terms of basic features (base composition and codon usage), the genes on plasmids were more similar to the chromosomal variable genes (distributed genes and unique genes) than to the chromosomal core genes. Although all the functional categories of the chromosomal genes were exhibited by the plasmid genes, the proportions of each category differed between these two gene sets. The 598 gene families shared between chromosomes and plasmids displayed a uniform distribution between the two groups. A phylogenetic analysis of the shared genes, including the chromosomal core gene set, indicated that gene exchange events between plasmids and chromosomes occurred frequently during the evolutionary histories of the strains and species in this group. Moreover, the shared genes between plasmids and chromosomes usually had different promoter and terminator sequences, suggesting that they are regulated by different elements at the transcriptional level. Conclusions We speculate that for the entire B. cereus group, adaptive genes are preserved on both plasmids and chromosomes; however, in a single cell, homologous genes on plasmids and the chromosome are controlled by different regulators to reduce the burden of maintaining redundant genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1206-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Ziyu Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Shiyun Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
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Liu X, Ruan L, Peng D, Li L, Sun M, Yu Z. Thuringiensin: a thermostable secondary metabolite from Bacillus thuringiensis with insecticidal activity against a wide range of insects. Toxins (Basel) 2014; 6:2229-38. [PMID: 25068925 PMCID: PMC4147579 DOI: 10.3390/toxins6082229] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 11/16/2022] Open
Abstract
Thuringiensin (Thu), also known as β-exotoxin, is a thermostable secondary metabolite secreted by Bacillus thuringiensis. It has insecticidal activity against a wide range of insects, including species belonging to the orders Diptera, Coleoptera, Lepidoptera, Hymenoptera, Orthoptera, and Isoptera, and several nematode species. The chemical formula of Thu is C22H32O19N5P, and it is composed of adenosine, glucose, phosphoric acid, and gluconic diacid. In contrast to the more frequently studied insecticidal crystal protein, Thu is not a protein but a small molecule oligosaccharide. In this review, a detailed and updated description of the characteristics, structure, insecticidal mechanism, separation and purification technology, and genetic determinants of Thu is provided.
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Affiliation(s)
- Xiaoyan Liu
- Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Palma L, Muñoz D, Berry C, Murillo J, Caballero P. Draft genome sequences of two Bacillus thuringiensis strains and characterization of a putative 41.9-kDa insecticidal toxin. Toxins (Basel) 2014; 6:1490-504. [PMID: 24784323 PMCID: PMC4052248 DOI: 10.3390/toxins6051490] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/21/2014] [Accepted: 04/24/2014] [Indexed: 11/16/2022] Open
Abstract
In this work, we report the genome sequencing of two Bacillus thuringiensis strains using Illumina next-generation sequencing technology (NGS). Strain Hu4-2, toxic to many lepidopteran pest species and to some mosquitoes, encoded genes for two insecticidal crystal (Cry) proteins, cry1Ia and cry9Ea, and a vegetative insecticidal protein (Vip) gene, vip3Ca2. Strain Leapi01 contained genes coding for seven Cry proteins (cry1Aa, cry1Ca, cry1Da, cry2Ab, cry9Ea and two cry1Ia gene variants) and a vip3 gene (vip3Aa10). A putative novel insecticidal protein gene 1143 bp long was found in both strains, whose sequences exhibited 100% nucleotide identity. The predicted protein showed 57 and 100% pairwise identity to protein sequence 72 from a patented Bt strain (US8318900) and to a putative 41.9-kDa insecticidal toxin from Bacillus cereus, respectively. The 41.9-kDa protein, containing a C-terminal 6× HisTag fusion, was expressed in Escherichia coli and tested for the first time against four lepidopteran species (Mamestra brassicae, Ostrinia nubilalis, Spodoptera frugiperda and S. littoralis) and the green-peach aphid Myzus persicae at doses as high as 4.8 µg/cm2 and 1.5 mg/mL, respectively. At these protein concentrations, the recombinant 41.9-kDa protein caused no mortality or symptoms of impaired growth against any of the insects tested, suggesting that these species are outside the protein’s target range or that the protein may not, in fact, be toxic. While the use of the polymerase chain reaction has allowed a significant increase in the number of Bt insecticidal genes characterized to date, novel NGS technologies promise a much faster, cheaper and efficient screening of Bt pesticidal proteins.
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Affiliation(s)
- Leopoldo Palma
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas-Universidad Pública de Navarra-Gobierno de Navarra, Campus Arrosadía, Mutilva Baja, Navarra 31192, Spain.
| | - Delia Muñoz
- Grupo de Protección Cultivos, Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Navarra 31006, Spain.
| | - Colin Berry
- Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff CF10 3AT, UK.
| | - Jesús Murillo
- Grupo de Protección Cultivos, Departamento de Producción Agraria, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Navarra 31006, Spain.
| | - Primitivo Caballero
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas-Universidad Pública de Navarra-Gobierno de Navarra, Campus Arrosadía, Mutilva Baja, Navarra 31192, Spain.
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Draft Genome Sequence of Highly Nematicidal Bacillus thuringiensis DB27. GENOME ANNOUNCEMENTS 2014; 2:2/1/e00101-14. [PMID: 24558243 PMCID: PMC3931364 DOI: 10.1128/genomea.00101-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we report the genome sequence of nematicidal Bacillus thuringiensis DB27, which provides first insights into the genetic determinants of its pathogenicity to nematodes. The genome consists of a 5.7-Mb chromosome and seven plasmids, three of which contain genes encoding nematicidal proteins.
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Zheng J, Peng D, Ruan L, Sun M. Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group. BMC Evol Biol 2013; 13:262. [PMID: 24295128 PMCID: PMC4219350 DOI: 10.1186/1471-2148-13-262] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 11/25/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. However, the origin and evolution of most plasmids remains unclear, especially for megaplasmids. Strains of the Bacillus cereus group contain up to 13 plasmids with genome sizes ranging from 2 kb to 600 kb, and thus can be used to study plasmid dynamics and evolution. RESULTS This work studied the origin and evolution of 31 B. cereus group megaplasmids (>100 kb) focusing on the most conserved regions on plasmids, minireplicons. Sixty-five putative minireplicons were identified and classified to six types on the basis of proteins that are essential for replication. Twenty-nine of the 31 megaplasmids contained two or more minireplicons. Phylogenetic analysis of the protein sequences showed that different minireplicons on the same megaplasmid have different evolutionary histories. Therefore, we speculated that these megaplasmids are the results of fusion of smaller plasmids. All plasmids of a bacterial strain must be compatible. In megaplasmids of the B. cereus group, individual minireplicons of different megaplasmids in the same strain belong to different types or subtypes. Thus, the subtypes of each minireplicon they contain may determine the incompatibilities of megaplasmids. A broader analysis of all 1285 bacterial plasmids with putative known minireplicons whose complete genome sequences were available from GenBank revealed that 34% (443 plasmids) of the plasmids have two or more minireplicons. This indicates that plasmid fusion events are general among bacterial plasmids. CONCLUSIONS Megaplasmids of B. cereus group are fusion of smaller plasmids, and the fusion of plasmids likely occurs frequently in the B. cereus group and in other bacterial taxa. Plasmid fusion may be one of the major mechanisms for formation of novel megaplasmids in the evolution of bacteria.
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Affiliation(s)
- Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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40
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Wang J, Mei H, Qian H, Tang Q, Liu X, Yu Z, He J. Expression profile and regulation of spore and parasporal crystal formation-associated genes in Bacillus thuringiensis. J Proteome Res 2013; 12:5487-501. [PMID: 24215520 DOI: 10.1021/pr4003728] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacillus thuringiensis, a Gram-positive endospore-forming bacterium, is characterized by the formation of parasporal crystals consisting of insecticidal crystal proteins (ICPs) during sporulation. We reveal gene expression profiles and regulatory mechanisms associated with spore and parasporal crystal formation based on transcriptomics and proteomics data of B. thuringiensis strain CT-43. During sporulation, five ICP genes encoded by CT-43 were specifically transcribed; moreover, most of the spore structure-, assembly-, and maturation-associated genes were specifically expressed or significantly up-regulated, with significant characteristics of temporal regulation. These findings suggest that it is essential for the cell to maintain efficient operation of transcriptional and translational machinery during sporulation. Our results indicate that the RNA polymerase complex δ and ω subunits, cold shock proteins, sigma factors, and transcriptional factors as well as the E2 subunit of the pyruvate dehydrogenase complex could cooperatively participate in transcriptional regulation via different mechanisms. In particular, differences in processing and modification of ribosomal proteins, rRNA, and tRNA combined with derepression of translational inhibition could boost the rate of ribosome recycling and assembly as well as translation initiation, elongation, and termination efficiency, thereby compensating for the reduction in ribosomal levels. The efficient operation of translational machineries and powerful protein-quality controlling systems would thus ensure biosyntheses of a large quantity of proteins with normal biological functions during sporulation.
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Affiliation(s)
- Jieping Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan, Hubei 430070, China
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Schulte RD, Makus C, Schulenburg H. Host-parasite coevolution favours parasite genetic diversity and horizontal gene transfer. J Evol Biol 2013; 26:1836-40. [PMID: 23865952 DOI: 10.1111/jeb.12174] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/04/2013] [Accepted: 03/28/2013] [Indexed: 10/26/2022]
Abstract
Host-parasite coevolution is predicted to favour genetic diversity and the underlying mechanisms (e.g. sexual reproduction and, more generally, genetic exchange), because diversity enhances the antagonists' potential for rapid adaptation. To date, this prediction has mainly been tested and confirmed for the host. It should similarly apply to the parasite. Indeed, our previous work demonstrated that experimental coevolution between the nematode Caenorhabditis elegans and its microparasite Bacillus thuringiensis selects for genetic diversity in both antagonists. For the parasite, the previous analysis was based on plasmid-encoded toxin gene markers. Thus, it was restricted to a very small part of the bacterial genome and did not cover the main chromosome, which harbours a large variety of virulence factors. Here, we present new data for chromosomal gene markers of B. thuringiensis and combine this information with the previous results on plasmid-encoded toxins. Our new results demonstrate that, in comparison with the control treatment, coevolution with a host similarly leads to higher levels of genetic diversity in the bacterial chromosome, thus indicating the relevance of chromosomal genes for coevolution. Furthermore, the frequency of toxin gene gain is significantly elevated during coevolution, highlighting the importance of horizontal gene transfer as a diversity-generating mechanism. In conclusion, our study emphasizes the strong influence of antagonistic coevolution on parasite genetic diversity and gene exchange.
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Affiliation(s)
- R D Schulte
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany.
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Wang P, Zhang C, Zhu Y, Deng Y, Guo S, Peng D, Ruan L, Sun M. The resolution and regeneration of a cointegrate plasmid reveals a model for plasmid evolution mediated by conjugation and oriT site-specific recombination. Environ Microbiol 2013; 15:3305-18. [PMID: 23826996 DOI: 10.1111/1462-2920.12177] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 05/26/2013] [Accepted: 06/01/2013] [Indexed: 11/30/2022]
Abstract
Cointegrate plasmids are useful models for the study of plasmid evolution if their evolutionary processes can be replicated under laboratory conditions. pBMB0228, a 17 706 bp native plasmid originally isolated from Bacillus thuringiensis strain YBT-1518, carries two nematicidal crystal protein genes, cry6Aa and cry55Aa. In this study, we show that pBMB0228 is in fact a cointegrate of two plasmids and contains two functional replication regions and two functional mobilization regions. Upon introduction into B. thuringiensis strain BMB171, pBMB0228 spontaneously resolves into two constituent plasmids via recombination at its oriT1 and oriT2 sites. The resolution does not require conjugation but can be promoted by conjugation. We further confirm that the resolution is mediated by oriT site-specific recombination requiring Mob02281 or Mob02282. Additionally, the two constituent plasmids of pBMB0228 are mobilizable, and can fuse back via oriT site-specific integration after entering into the same cell by conjugation. Our study confirms that native plasmid can reversibly interconvert between a cointegrate structure and its constituent plasmids. This study provides insight into the evolution of cointegrate plasmids, linking plasmid evolution with conjugation and the oriT site-specific recombination function of relaxase.
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Affiliation(s)
- Pengxia Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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High-throughput identification of promoters and screening of highly active promoter-5'-UTR DNA region with different characteristics from Bacillus thuringiensis. PLoS One 2013; 8:e62960. [PMID: 23675447 PMCID: PMC3651082 DOI: 10.1371/journal.pone.0062960] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/27/2013] [Indexed: 01/05/2023] Open
Abstract
In bacteria, both promoters and 5'-untranslated regions (5'-UTRs) of mRNAs play vital regulatory roles in gene expression. In this study, we identified 1203 active promoter candidates in Bacillus thuringiensis through analysis of the genome-wide TSSs based on the transcriptome data. There were 11 types of σ-factor and 34 types of transcription factor binding sites found in 723 and 1097 active promoter candidates, respectively. Moreover, within the 1203 transcriptional units (TUs), most (52%) of the 5'-UTRs were 10-50 nucleotides in length, 12.8% of the TUs had a long 5'-UTR greater than 100 nucleotides in length, and 16.3% of the TUs were leaderless. We then selected 20 active promoter candidates combined with the corresponding 5'-UTR DNA regions to screen the highly active promoter-5'-UTR DNA region complexes with different characteristics. Our results demonstrate that among the 20 selected complexes, six were able to exert their functions throughout the life cycle, six were specifically induced during the early-stationary phase, and four were specifically activated during the mid-stationary phase. We found a direct corresponding relationship between σ-factor-recognized consensus sequences and complex activity features: the great majority of complexes acting throughout the life cycle possess σ(A)-like consensus sequences; the maximum activities of the σ(F)-, σ(E)-, σ(G)-, and σ(K)-dependent complexes appeared at 10, 14, 16, and 22 h under our experimental conditions, respectively. In particular, complex Phj3 exhibited the strongest activity. Several lines of evidence showed that complex Phj3 possessed three independent promoter regions located at -251∼-98, -113∼-31, and -54∼+14, and that the 5'-UTR +1∼+118 DNA region might be particularly beneficial to both the stability and translation of its downstream mRNA. Moreover, Phj3 successfully overexpressed the active β-galactosidase and turbo-RFP, indicating that Phj3 could be a proper regulatory element for overexpression of proteins in B. thuringiensis. Therefore, our efforts contribute to molecular biology research and the biotechnological application of B. thuringiensis.
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Transcriptional regulation and characteristics of a novel N-acetylmuramoyl-L-alanine amidase gene involved in Bacillus thuringiensis mother cell lysis. J Bacteriol 2013; 195:2887-97. [PMID: 23603740 DOI: 10.1128/jb.00112-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Bacillus thuringiensis, a novel N-acetylmuramoyl-L-alanine amidase gene (named cwlB) was detected, and the CwlB protein was purified and characterized. Reverse transcription-PCR (RT-PCR) results indicated that cwlB and an upstream gene (named cwlA) formed one transcriptional unit. 5' rapid amplification of cDNA ends (5'-RACE)-PCR and transcriptional fusions with the lacZ gene indicated that transcription of the operon was directed by a promoter, P(cwlA), which is located upstream from the cwlA gene and that the transcription start site is a single 5'-end nucleotide residue T located 25 nucleotides (bp) upstream from the cwlA translational start codon. Moreover, the activity of P(cwlA) was controlled by σ(K). Morphological analysis suggested that the mutation of cwlB could delay spore release compared to the timing of spore release in the wild-type strain. Western blot assay demonstrated that purified CwlB bound to the B. thuringiensis cell wall. Observations with laser confocal microscopy and a green fluorescent protein-based reporter system demonstrated that the CwlB protein localizes to the cell envelope. All results suggest that the CwlB protein is involved in mother cell lysis in B. thuringiensis.
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Zhou J, Xu Z, Chen S. Simulation and prediction of the thuringiensin abiotic degradation processes in aqueous solution by a radius basis function neural network model. CHEMOSPHERE 2013; 91:442-447. [PMID: 23273880 DOI: 10.1016/j.chemosphere.2012.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/24/2012] [Indexed: 06/01/2023]
Abstract
The thuringiensin abiotic degradation processes in aqueous solution under different conditions, with a pH range of 5.0-9.0 and a temperature range of 10-40°C, were systematically investigated by an exponential decay model and a radius basis function (RBF) neural network model, respectively. The half-lives of thuringiensin calculated by the exponential decay model ranged from 2.72 d to 16.19 d under the different conditions mentioned above. Furthermore, an RBF model with accuracy of 0.1 and SPREAD value 5 was employed to model the degradation processes. The results showed that the model could simulate and predict the degradation processes well. Both the half-lives and the prediction data showed that thuringiensin was an easily degradable antibiotic, which could be an important factor in the evaluation of its safety.
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Affiliation(s)
- Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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Wang J, Mei H, Zheng C, Qian H, Cui C, Fu Y, Su J, Liu Z, Yu Z, He J. The metabolic regulation of sporulation and parasporal crystal formation in Bacillus thuringiensis revealed by transcriptomics and proteomics. Mol Cell Proteomics 2013; 12:1363-76. [PMID: 23408684 DOI: 10.1074/mcp.m112.023986] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacillus thuringiensis is a well-known entomopathogenic bacterium used worldwide as an environmentally compatible biopesticide. During sporulation, B. thuringiensis accumulates a large number of parasporal crystals consisting of insecticidal crystal proteins (ICPs) that can account for nearly 20-30% of the cell's dry weight. However, the metabolic regulation mechanisms of ICP synthesis remain to be elucidated. In this study, the combined efforts in transcriptomics and proteomics mainly uncovered the following 6 metabolic regulation mechanisms: (1) proteases and the amino acid metabolism (particularly, the branched-chain amino acids) became more active during sporulation; (2) stored poly-β-hydroxybutyrate and acetoin, together with some low-quality substances provided considerable carbon and energy sources for sporulation and parasporal crystal formation; (3) the pentose phosphate shunt demonstrated an interesting regulation mechanism involving gluconate when CT-43 cells were grown in GYS medium; (4) the tricarboxylic acid cycle was significantly modified during sporulation; (5) an obvious increase in the quantitative levels of enzymes and cytochromes involved in energy production via the electron transport system was observed; (6) most F0F1-ATPase subunits were remarkably up-regulated during sporulation. This study, for the first time, systematically reveals the metabolic regulation mechanisms involved in the supply of amino acids, carbon substances, and energy for B. thuringiensis spore and parasporal crystal formation at both the transcriptional and translational levels.
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Affiliation(s)
- Jieping Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PRC
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47
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Complete Genome Sequence of Bacillus thuringiensis Strain 407 Cry-. GENOME ANNOUNCEMENTS 2013; 1:genomeA00158-12. [PMID: 23405326 PMCID: PMC3569317 DOI: 10.1128/genomea.00158-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 11/30/2012] [Indexed: 11/25/2022]
Abstract
Bacillus thuringiensis is an insect pathogen that has been used widely as a biopesticide. Here, we report the genome sequence of strain 407 Cry-, which is used to study the genetic determinants of pathogenicity. The genome consists of a 5.5-Mb chromosome and nine plasmids, including a novel 502-kb megaplasmid.
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48
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January – June 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2044675] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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